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Plugin to use Locscale program within the Scipion framework

Project description

This plugin provides a wrapper around LocScale program for local sharpening of cryo-EM density maps.

PyPI release License Supported Python versions SonarCloud quality gate Downloads

Installation

You will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:

  1. Stable version

    scipion installp -p scipion-em-locscale
  2. Developer’s version

    • download repository

    git clone -b devel https://github.com/scipion-em/scipion-em-locscale.git
    • install

    scipion installp -p path/to/scipion-em-locscale --devel

LocScale sources will be downloaded automatically with the plugin, but you can also link an existing installation. Default installation path assumed is software/em/locscale-0.1, if you want to change it, set LOCSCALE_HOME in scipion.conf file to the folder where the LocScale is installed. LocScale uses EMAN2 libraries, so you need to provide existing EMAN2 installation path by setting EMAN2_HOME variable (default eman-2.99) in the config file.

Note: mpi4py will be installed in the Eman’s python

Note2: File locscale-0.1/source/locscale_mpi.py has been patched (see locscale_mpi.py.patch) to be able to work with new versions of EMAN

To check the installation, simply run the following Scipion tests:

scipion test locscale.tests.test_protocol_locscale.TestProtLocscale

A complete list of tests can also be seen by executing scipion test --show --grep locscale

Supported versions

0.1

Protocols

  • local sharpening

References

  1. Jakobi A. et al., eLife, 2017

Project details


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